Additional Superintendent of Police Rajiv Malhotra said that a student was sodomised by the Imam of the mosque on Monday after which he was arrested.
He said another Imam was appointed in the place of the accused, which resulted in a clash as he belonged to another sect.
The two groups indulged in brick-batting which led to chaos in the area and the market remain closed, the ASP said.
Heavy police force was deployed in the area to prevent any untoward incident.